June 8, 2011 | Playing to the home crowd, “open science” advocate Jonathan Eisen, an evolutionary geneticist and professor in the Genome Center at University of California, Davis, received the 2011 Benjamin Franklin Award sporting a Boston Red Sox baseball jersey with “PLOS 1” on the back—a neat plug for the academic editor-in-chief of PLoS Biology.
The award, presented by Bioinformatics Organization president Jeff Bizarro, was not the first given to the Eisen clan. Jonathan’s brother Michael won the first Franklin award in 2002.
Explaining the shirt, Eisen noted that both he and Franklin were born in Boston. But Boston is also where the “relationship between science and freedom” took root, he said. “Science is about sharing of ideas and information... What we’ve done, unfortunately, is create a bunch of social structures that inhibit the openness in part of science.”
Michael Eisen was a co-founder of the Public Library of Science with Pat Brown and Harold Varmus, which advocates open access and publishes papers under a broad creative commons license. Eisen recalled the original open access petition was signed by 100,000 scientists, including Claire Fraser, his former boss at The Institute for Genomic Research, but had very little effect. And so PLoS went from being a petition to a journal publisher.
Eisen also acknowledged former Franklin Awardee Sean Eddy (HHMI Janelia Farm), who had said the reason to fund genome sequencing projects was to provide data to the community. “This resonated with me,” said Eisen. “I started releasing data without restrictions.”
The final event that convinced Eisen of the need for open science was a family emergency. A few years ago, doctors performed a “botched amniocentesis” on Eisen’s wife, who was hospitalized for weeks. “I logged on at 2 in the morning from my wife’s hospital room,” he said, desperate to search for information on her condition. “I couldn’t get access... I couldn’t read the literature that my tax money had paid for. That was it. I completely changed after that moment to being an open science advocate. It was ludicrous that I could not have access to that information. I had to pay $30/article without knowing if they were relevant.”
Eisen told Bio•IT World he was delighted to fend off intense competition from five other candidates (see, “Franklin Five Short List”) to win this year’s award, especially after being short-listed in 2009, though he said Phil Bourne fully deserved the award that year. Eisen uses his high visibility in social media, notably his popular “Tree of Life” blog, to advocate for open access in science publishing and data release. He has been involved with numerous freely available software packages, including AMPHORA and PhyloOTU. He also helped release a new open data sharing tool for scientists called BioTorrents, to encourage scientists to share data and results. •
Franklin Five Short List
The other five open-access evangelists short-listed for the 2011 Franklin Award were:
Gary Bader (The Donnelly Centre, University of Toronto)
Computational biologist who developed the Biomolecular Interaction Network Database (BIND). Also plays an active role in the development of biological pathway and network data exchange formats such as BioPAX, Pathway Commons and Cytoscape visualization software.
Eugene Koonin (NCBI)
Leader of the evolutionary genomics research group at NCBI, Koonin is co-founder of Biology Direct, which champions signed peer review. His organization of the Clusters of Orthologous Groups (COG) project opened up the field of comparative genomics.
John Quackenbush (Harvard School of Public Health/Dana Farber Cancer Institute)
Quackenbush has promoted open-source and publicly available software tools in computational biology, particularly gene expression tools, for more than a decade.
Steven Salzberg (University of Maryland)
Salzberg has developed widely used computational tools for genome assembly, gene prediction, and genome comparison, including Glimmer, Bowtie, TopHat, MUMmer, and JIGSAW. He actively campaigns against software and gene patents.
Alex Zhavoronkov (Johns Hopkins University)
Zhavoronkov helped establish the International Aging Research Portfolio (IARP), an independent non-profit initiative serving the aging research community worldwide.